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PRISM

http://compbio.cs.toronto.edu/prism/

PRISM is a software for split read (reads which span across a structrual variant -- SV ) mapping and SV calling from the mapping result. PRISM is able to detect small insertions and abitrary size deletions, inversions and tandom duplications with the direction of discordant read pairs. PRISM_CTX is a tool for detecting inter-chromosome trans-location events. 

PRISM and PRISM_CTX were originally designed and written by Michael Brudno and Yue Jiang, The original PRISM publication can be found here

The authors may be contacted via e-mail at: prism at cs.toronto.edu

Additional information is available in the PRISM README file and PRISM_CTX README file. 

http://compbio.cs.toronto.edu/prism/